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- PDB-1a32: RIBOSOMAL PROTEIN S15 FROM BACILLUS STEAROTHERMOPHILUS -

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Basic information

Entry
Database: PDB / ID: 1a32
TitleRIBOSOMAL PROTEIN S15 FROM BACILLUS STEAROTHERMOPHILUS
ComponentsRIBOSOMAL PROTEIN S15
KeywordsRIBOSOMAL PROTEIN / MULTIWAVELENGTH ANOMALOUS DIFFRACTION / PROTEIN-RNA / RIBOSOMAL PROTEIN INTERACTIONS / RIBOSOME / RNA-BINDING
Function / homology
Function and homology information


cytosolic small ribosomal subunit / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
S15/NS1, RNA-binding / Ribosomal protein S15, bacterial-type / Helix Hairpins / Ribosomal protein S15 signature. / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / S15/NS1, RNA-binding / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Small ribosomal subunit protein uS15
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsClemons Junior, W.M. / Davies, C. / White, S.W. / Ramakrishnan, V.
CitationJournal: Structure / Year: 1998
Title: Conformational variability of the N-terminal helix in the structure of ribosomal protein S15.
Authors: Clemons Jr., W.M. / Davies, C. / White, S.W. / Ramakrishnan, V.
History
DepositionJan 27, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBOSOMAL PROTEIN S15


Theoretical massNumber of molelcules
Total (without water)10,5861
Polymers10,5861
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.020, 33.750, 75.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RIBOSOMAL PROTEIN S15


Mass: 10586.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Cell line: BL21 / Cellular location: RIBOSOME / Plasmid: PET-13A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P05766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38 %
Crystal growpH: 6.5 / Details: 3.0M NA/K PHOSPHATE PH 6.5
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: unknown
Components of the solutions
*PLUS
Conc.: 2.4-3.0 M / Common name: Na/KPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. obs: 139136 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 12
Reflection shellResolution: 2.05→2.13 Å / Redundancy: 5 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 3 / Rsym value: 0.379 / % possible all: 99.2
Reflection shell
*PLUS
Rmerge(I) obs: 0.343

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→6 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.318 369 10 %RANDOM
Rwork0.212 ---
obs0.212 3808 99.64 %-
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms717 0 0 59 776
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.14
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.31 64 11.1 %
Rwork0.345 575 -
obs--99.5 %
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.345

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